Credit: NPG

Most genome-wide association studies (GWASs) of complex diseases have so far focused on the identification of genes associated with disease susceptibility. But little is known about whether genetics contribute to disease prognosis — that is, the course that a disease takes following its initial emergence. Reporting in Cell, Smith and colleagues describe a non-coding single-nucleotide polymorphism (SNP) in the gene encoding forkhead box protein O3 (FOXO3; also known as FOXO3A), the minor allele of which is associated with a milder course of Crohn's disease and rheumatoid arthritis, and with an increased risk of developing severe malaria.

Using phenotypic data, the authors identified subgroups of patients who had either aggressive or indolent Crohn's disease in an existing large GWAS cohort. Detailed genetic analysis of the GWAS data sets for these subgroups showed the presence of an intronic SNP within FOXO3 (rs12212067: T→G) that associated with disease prognosis but not with susceptibility; the minor (G) allele was consistently more common in patients with indolent Crohn's disease.

But how does genetic variation at this locus influence disease prognosis? The authors showed that lipopolysaccharide (LPS)-stimulated monocytes from heterozygous individuals had a twofold increase in transcription of FOXO3 from the minor (G) allele compared with the major (T) allele. Following in vitro stimulation with various pathogen-associated molecular patterns, monocytes from healthy individuals who are homozygous for the minor (G) allele produced lower levels of the pro-inflammatory cytokines tumour necrosis factor (TNF), interleukin-1β (IL-1β), IL-6 and IL-8 and higher levels of the anti-inflammatory cytokine IL-10 than monocytes from major (T) allele homozygotes. This suggests that differences in FOXO3 transcription influence the cytokine milieu produced by monocytes. But how?

The function of FOXO3 is mainly controlled by the regulation of its retention within, or exclusion from, the nucleus. Translocation of FOXO3 out of the nucleus results in an increase in TNF production, whereas its subsequent re-accumulation in the nucleus (termed nuclear recovery) correlates with decreased TNF and increased IL-10 production. The authors found that the nuclear recovery phase occurred more rapidly in LPS-stimulated monocytes from minor (G) allele homozygotes than in those from major (T) allele homozygotes, and this correlated with an earlier reduction in TNF production and an earlier increase in IL-10 production.

earlier nuclear recovery of FOXO3 in monocytes from minor (G) allele homozygotes induces higher TGFβ1 production

Further investigations showed that monocytes from minor (G) allele homozygotes produced more transforming growth factor-β1 (TGFβ1) than those from major (T) allele homozygotes; blocking TGFβ1 signalling abolished the genotype-specific differences in TNF and IL-10 production. FOXO3 was shown to directly interact with the TGFB1 promoter, and silencing of FOXO3 in two different human monocyte cell lines reduced transcription of TGFB1. This suggests that the earlier nuclear recovery of FOXO3 in monocytes from minor (G) allele homozygotes induces higher TGFβ1 production, which in turn modulates TNF and IL-10 production.

To further support a link between altered FOXO3 function and intestinal inflammation, the authors induced colitis using dextran sodium sulphate in mice with a missense mutation in Foxo3. Reduced Foxo3 activity predisposed these mice to more severe colitis and was associated with increased TNF and decreased IL-10 production.

Finally, the authors found an association between the minor (G) allele of FOXO3 and a milder course of rheumatoid arthritis. This allele was also associated with an increased susceptibility to severe malaria in cohorts of Kenyan and Vietnamese patients, which is consistent with the negative effect of low TNF and high IL-10 production on parasite clearance.

So, a genetic polymorphism in FOXO3 that limits inflammatory responses by reducing pro-inflammatory cytokine production while increasing IL-10 production is associated with the prognosis of distinct inflammatory and infectious diseases.